Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing

Abstract

Summary: We present Mutascope, a sequencing analysis pipeline specifically developed for the identification of somatic variants present at low-allelic fraction from high-throughput sequencing of amplicons from matched tumor-normal specimen. Using datasets reproducing tumor genetic heterogeneity, we demonstrate that Mutascope has a higher sensitivity and generates fewer false-positive calls than tools designed for shotgun sequencing or diploid genomes.

Availability: Freely available on the web at http://sourceforge.net/projects/mutascope/.

Contact: oharismendy@ucsd.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Mutascope principle and performance. (a) The sequencing error rate varies based on the read type (blue and red), position in the read (x-axis) or reference base sequenced (lines). (b) Paired reads (red and blue) from shotgun and amplicon sequencing distribute differently over the targeted region (gray box) resulting in different consensus error rates (right panel). (c–e) Comparison of 4–6 tools by ROC analysis showing the classification of mutations at low-allelic fraction (1–10%) in the MIX samples (c), after down-sampling reads to 50 or 10% of maximum coverage (d), or using 1 and 10% allelic fraction variants from TNS pairs. (f) Evolution of the true-positive rate and positive predicted value from the MIX sample low-allele frequency variants (1–10%) before (dotted line) and after (continuous line) application of high-confidence filters